Rogier Versteeg ^{1, @}, Barbera D.C. van Schaik ^{1, 2}, Marinus F. van Batenburg ^{4, 5}, Marco Roos ¹, Ramin Monajemi ², Huib Caron ^{1, 3}, Harmen J. Bussemaker ⁵ and Antoine H.C. van Kampen ²

¹ Department of Human Genetics, Academic Medical Center, University of Amsterdam, 1100DE Amsterdam, The Netherlands;
² Department of Bioinformatics, Academic Medical Center, University of Amsterdam, 1100DE Amsterdam, The Netherlands;
³ Department of Paediatric Oncology/EKZ, Academic Medical Center, University of Amsterdam, 1100DE Amsterdam, The Netherlands;
⁴ Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands;
⁵ Department of Biological Sciences and Center for Computational Biology and Bioinformatics, Columbia University, New York 10027, USA

^@ Corresponding author:
E-mail:    R.Versteeg@AMC.UVA.NL              FAX:  + 0031-20-6918626.

The chromosomal gene expression profiles established by the Human Transcriptome Map (HTM) revealed a clustering of highly expressed genes in about 30 domains, called ridges. To physically characterize ridges, we constructed a new HTM based on the draft human genome sequence (HTMseq). Expression of 25,003 genes can be analyzed online in a multitude of tissues (http://bioinfo.amc.uva.nl/HTMseq). Ridges are found to be very gene-dense domains with a high GC content, a high SINE repeat density, and a low LINE repeat density. Genes in ridges have significantly shorter introns than genes outside of ridges. The HTMseq also identifies a significant clustering of weakly expressed genes in domains with fully opposite characteristics (antiridges). Both types of domains are open to tissue-specific expression regulation, but the maximal expression levels in ridges are considerably higher than in antiridges. Ridges are therefore an integral part of a higher order structure in the genome related to transcriptional regulation.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1649303. Article published online before print in August 2003.

[Supplemental material is available online at www.genome.org. The HTMseq application is available online at
http://bioinfo.amc.uva.nl/HTMseq]. 

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